Projects awarded with response mode funds

1. Chris Willberg and Paul Klenerman

► Expression and characterisation of lectin-like transcript 1 in lymphoid tissues in uninflamed and inflamed bowel

The gut must carefully balance responses directed against pathogens and tolerance against dietary material and commensal microbial products. It achieves this by inducing specialised immune structures (lymphoid tissues), such as Peyer’s Patches and isolated lymphoid follicles. Within these structures, local T and B cell responses can develop towards any potential pathogen. Under conditions of chronic inflammation, such as inflammatory bowel disease, a third structure, tertiary lymphoid tissues, are observed. Questions about these tissues remain unanswered; are their presence the cause or consequence of immune dysregulation within the gut?

A focus of our group has been on the receptor, lectin-like transcript (LLT-) 1. We have recently described LLT-1 distribution within different body tissues and its high levels in B cell follicles within the tonsils and spleens. However, the presence of LLT-1 within the unique lymphoid tissues of the gut has not been explored.

Here we propose to use a novel microscopy technique, chip-cytometry, to assess LT-1 within the gut and to make a detailed analysis of the cellular components of these tissues compared to those seen within the tonsils. We hypothesise that the presence of LLT-1 within the gut will identify both early and mature lymphoid tissues. This small study will generate a novel data set that will have aetiological and prognostic implications, and will form the basis for future funding applications. Furthermore, the work will result in the standardising of practical techniques and analytical pipelines that will be of benefit across the BRC3 theme where chip-cytometry is a critical component.

2. Irina Udalova and Simon Travis

► Therapeutic potential of inhibitors in Ulcerative Colitis

Inflammatory bowel disease (IBD) is a group of inflammatory conditions including ulcerative colitis (UC). The use of biological therapies has radically improved disease prognosis for many patients, but approximately 30% of patients do not respond to anti-TNF treatment and around half of treated patients become anti-TNF refractory. In addition, biologics-based therapies carry a high economic cost for health services

The success of kinase inhibitors in the treatment of cancer, coupled with a greater understanding of inflammatory signalling cascades, led to kinase inhibitors taking centre stage in the pursuit for new anti-inflammatory agents. The JAK kinase inhibitor Tofacitinib has proved effective in treating moderate-severe UC and other JAK inhibitors are under study in Oxford and elsewhere.

This proposal aims to set up a pre-clinical assessment of another kinase inhibitor, which demonstrated an acceptable safety profile in early phase clinical trials for metastatic cancer and solid tumors. Our early data implicate that the signalling pathway it targets in the regulation of pro-inflammatory cytokine release and in the pathogenesis of colitis in a mouse model. Thus, the results of this project may lay the ground for possible re-purposing of this inhibitor for UC and other inflammatory diseases.

3. John Ryan

► The role of iron in gastrointestinal disease and inflammation

Iron is a micronutrient critical to several important processes in the body, such as the generation of energy and oxygen transport. However iron levels must be tightly controlled to avoid toxicity due to excess. The liver controls iron by secreting a hormone to reduce iron absorption from the gut and iron release from immune cells. Disruption of this control can lead to abnormal iron build up in tissues such as the liver, the pancreas, and fat, which results in disease. For example, iron plays a part in the development of inflammation and cancer of both the liver and large bowel, and in the development of diabetes.

The aim of this work is to explore how the liver, gut microbiome and adipose tissue​ interact to control iron, and how this impacts on disease. Select groups of patients who have problems with iron metabolism have been identified, with detailed clinical information kept alongside blood and tissue samples. Patients are followed through treatment of their condition to examine how changes in iron can link to changes in their disease, so that new therapeutic approaches can be discovered.

4. Smita Patel

► The role of SAMD9L in primary immunodeficiency and immune dysregulation

We have identified novel mutations in SAMD9L in patients with an immune dysregulatory and neurological phenotype by whole genome sequencing in collaboration with the WTCHG. This gene has recently been identified in 4 families with ataxia pancytopenia syndrome- but little is known about the gene function and its role in the immune system. The immune defects in the few reported patients are not well defined. We propose to investigate the effect of these genetic variants by initially studying protein expression and function of SAMD9L. We will go on to undertake single cell sequencing of mucosal cells, white bloods cells and cell lines from the patient to understand the role of normal and mutated SAMD9L in different pathways. Using this multiomic approach we hope define a molecular signature for the disease, develop a diagnostic test and identify potential pathways amenable to drug therapy.

Inflammatory bowel disease (IBD), in its manifestations Crohn’s disease and ulcerative colitis, is a chronic inflammatory disease that can affect all parts of the digestive tract. Environmental factors, genetic predisposition and an abnormal function of the immune system are thought to cause IBD. Standard therapies aim at controlling intestinal inflammation and prolonging the time between disease flare-ups. Although significant progress has been made over the last decades, a high proportion of patients still do not respond to these anti- inflammatory therapies, or become resistant during the course of treatment. Failure to therapeutically control chronic inflammation can lead to severe complications in IBD patients, such as fibrosis, which requires surgical intervention. Fibrotic changes in the intestine are driven by an activation of a particular cell type, the fibroblast.

The aim of this project is to find out whether IBD patients that go on to require surgery display an activation of fibroblasts, and which changes in the tissue are associated with this activation. For this, differences in the way the surgically removed fibrotic tissue is programmed will be compared to the programming of non-inflamed ‘normal’ tissue. We believe that certain alterations in this programming, which is controlled by a network of signals, can lead to changes that are specifically associated with inflammation and the requirement for surgery. Differences in the networks of signals which make up this program of inflamed and non-inflamed tissue will help us identify novel, fibroblast-targeting, therapies which will disrupt the inflammation program and hopefully reduce the requirement for surgery.

6. Oliver Brain and Alison Simmons

► Prediction and prevention of immunotherapy side-effects: PRISE

The treatment of malignancy has developed to include medications that affect the immune system. These treatments block the action of so called ‘check-point’ proteins, whose usual function is to prevent immune overactivation and thus limit the chance of unwanted inflammation. Whilst these drugs are a critical treatment for malignancies with previously very limited therapeutic options (such as metastatic melanoma, non-small cell lung cancer, renal cell carcinoma), they have a side-effect profile in keeping with immune system activation. This means that they can result in unwanted inflammation at other sites, and frequently this affects the gastrointestinal (GI) tract or bowel. The frequency of this gastrointestinal inflammation (or enterocolitis) varies based on the drug and the dose used, but typically diarrhoea occurs in the region of 20-45% of treated patients. These side effects are an important cause of patient distress, and occasionally of life-threatening complications such as bowel perforation. The enterocolitis currently requires systemic immunosuppression and also results in the interruption and often cessation of these critical anti-cancer therapies.

Our study will be the first to prospectively investigate these side-effects with a particular focus on colitis. This project will assess the environmental, immune and gut microorganism effects on colitis development. The aims of the study are to understand the aetiology of this colitis such that it enables improved prevention and treatment in this vulnerable cohort, whilst also furthering our understanding of the GI immune system in a defined clinical setting. The project is managed in Oxford TGU and will be delivered through a novel collaboration with our oncology colleagues.

7. Consuelo Anzilotti, Simon Davies and Richard Cornall

► New approaches to treating colitis: inhibitory superagonists

When the immune system of an individual cannot distinguish cells of its own from pathogens causing disease, a condition called autoimmunity can develop. In this condition, strategies designed to eliminate pathogens are used by cells of the immune system to attack cells or organs of the human body, causing inflammation. Inflammation can target many different organs and in the vast majority of cases is a chronic process which, if left untreated, can lead to permanent organ damage and sometimes death. The intestine is often a target of autoimmunity: colitis affects ~3 million young adults worldwide and has a major impact on quality of life and economic productivity.

The inflammatory activity of immune cells is regulated by soluble substances or by interactions with other cell types, and we can mimic the effects of the cellular interactions using molecules called antibodies, which bind specifically to receptors displayed on the surface of immune cells. We have developed a variety of antibodies binding several of those receptors and we aim to test their efficacy in screening assays with the objective of identifying new drugs for the treatment of colitis.

We are also interested in discovering other surface molecules that can contribute to the disease, and to do so we will perform detailed analysis of cells derived from healthy or inflamed colonic tissue: this will allow us to better understand how the disease develops and to identify new therapeutic targets.

8. Simon Travis and Satish Keshav

► Patient partnership pathways in IBD clinical care

Patients with inflammatory bowel disease experience unpredictable episodes of relapse and similarly unpredictable periods of remission. Conventional outpatient care, with clinic visits every 3-12 months, does not capture the true burden of symptoms, since visits infrequently coincide with episodes of active disease. This leads to delays in treatment, failure to optimise maintenance therapy and suboptimal use of clinic resources.

Pathways to care need to change. TrueColours UC has been developed in Oxford to allow patients maintain symptom diaries in real time, collect quality of life data using the simple IBD Control questionnaire and record internationally agreed (www.ichom.org) patient-related outcomes. Funding has been sourced for a Clinical Fellow (Norman Collisson Foundation) and from Industry for a network manager to facilitate roll out of the scheme across hospitals in the Oxford AHSN (clinical lead John Gordon, Winchester). What is needed to make this happen at participating hospitals is an IT-savvy healthcare professional, who can introduce patients to the system on site at the 5 participating hospitals and provide direct support for queries.

This will be the first time that realtime data and outcomes have been measured for UC, which can be linked to biological data (machine learning) and use of health care resources, to identify patients for potential clinical trials and redesign patient pathways.

► An investigation into the stability of the adaptive and innate immune compartments within a transplanted small bowel: A pilot study

Intestinal failure, where the gut fails to absorb sufficient nutrients, is a debilitating condition which requires treatment with intravenous parenteral nutrition. Unfortunately, this treatment can be complicated by severe infections and venous blood clots, and in such circumstances intestinal transplantation can be an effective treatment. However intestinal transplantation suffers from high rates of graft rejection, as well as cases of graft versus host disease (GVHD) and has only a 60% 5-year survival.

Large numbers of immune cells from the donor are transferred into an intestinal transplant, and the interactions of the immune cells from donor and recipient, the survival of donor immune cells in the transplant, and the mechanisms that allow colonisation of the transplanted tissue by recipient immune cells are not well understood. Our work will study these questions through studying intestinal immune cell populations in recipients of intestinal transplants at the Oxford University Hospitals NHS Foundation Trust transplantation unit, one of only two centres offering adult intestinal transplantation in the United Kingdom. These results will have direct patient benefit by elucidating the mechanisms that drive graft rejection and GVHD in intestinal transplantation, and by identifying strategies that might prevent these complications. Moreover, these results may provide insights into more fundamental questions in human immunology, including the dynamics of tissue residency of immune cells in the gut.

► Enteric viral infection in childhood and coeliac disease

Coeliac disease is a common immune condition where susceptible individuals develop inflammation of the gut in response to gluten, a protein in wheat. Whilst genetics play an important role in the development of coeliac disease, there is evidence that an environmental trigger is required for coeliac disease to develop. Circumstantial evidence has suggested that viral infections in childhood could be that trigger, but definitive proof remains elusive. A recent study has suggested that reovirus, a virus affecting the gut that generally causes no symptoms, can trigger a condition like coeliac disease in mice under experimental conditions, however it remains unclear if this infection is associated with coeliac disease in humans. The discovery of infections that can trigger coeliac disease could have a profound impact on the prevention of the development of coeliac disease, as well as on the prevention of diseases associated with it, such as Type 1 Diabetes.

We will test the association between reovirus, along with a number of other viral infections that affect the gut, and the development of coeliac disease by using stored samples from a recent study of diagnostic methods of coeliac disease in children. This large, well-described, cohort of children with and without coeliac disease provides an ideal group in which to test for an association between viral infection and coeliac disease. We will perform tests to measure antibody responses to these viruses in children with and without coeliac disease.

Inflammatory bowel disease (IBD) is a group of conditions characterized by chronic inflammation of the gut. IBD is sub-classified as Crohn’s Disease (CD), Ulcerative Colitis (UC) or Inflammatory Bowel Disease Unclassified (IBD-U). In the majority of patients, the genetic architecture suggests a polygenic contribution. In rare patients with the most severe phenotypes (extreme early age onset, non-responsiveness to therapy and extra intestinal manifestations) monogenic forms of IBD have been identified. Several technologies have been used to detect these variants including target gene panel sequence (TGPS), Whole Exome Sequencing (WES) and Whole Genome Sequencing (WGS). Each technology has inherent strengths and weaknesses for scientific and clinical applications and timing of the analysis is a major issue for clinically relevant decision making. TGPS is a reliable and comparably cheap sequencing technology to ensure good sequencing coverage, fast turnaround, and reasonable costs. We will use of a pre-designed panel containing clinically relevant monogenic IBD genes to facilitate the identification of these rare monogenic patients in Oxford. The benefits to patients include a more rapid candidate identification for subsequent clinical validation allowing effective clinical management of patients through personalised medicine”.

12. Alessandra Geremia, Bruno Sgromo and Carolina Arancibia

► Microbial-host interactions involved in obesity and the response to bariatric surgery

Obesity has reached alarming levels in the UK. According to a government report, one in four adults are obese in the UK. Medical and dietary interventions are often ineffective at inducing weight loss and the best outcomes are obtained after weight loss surgery (also known as bariatric surgery). These surgical procedures were initially thought to work mechanistically through stomach restriction and lower calorie absorption through the shortened intestine. However, recent evidence has challenged this concept and it has been suggested that changes in the gut microbial flora could affect metabolism contributing to weight loss and increased insulin response. Gut flora is beneficial to the host in many ways, contributing to for example, nutrient absorption and a healthy immune system. Abnormalities in the composition of the gut microbes are thought to contribute to the pathology of certain diseases, including obesity and diabetes.

The aim of this project is to find out how altered host and microbial functions affect weight loss and metabolism after bariatric surgery. Understanding more about the microbial flora and how this impacts patient’s health will hopefully make way for new approaches in the treatment of obesity and diabetes.